Graymachine takes a quick look in a new tutorial, Rendering AE Projects with Adobe Media Encoder.
AME has some newer advantages (the H.264 codec is a win), though you'll have to determine the best options for your particular circumstance. One would hope that someday AME will mimic the AE Render Que more (or the long defunct Movie Cleaner Pro), and expose finer control over codec settings, especially for H.264.
Don't forget that you can background render AE projects using Adobe Media Encoder -- but you have to drag projects directly into the AME render list [even in CS6]. Here's Harry:
Also, Topher Welsh notes that AME also give you the render file size if that a concern, and you can skip about the presets to find an appropriate size,
For more options and info on rendering in After Effects, see Background rendering with After Effects and other posts tagged render and background rendering.
Note: Kevin Monahan posted some new info and resources in
Exporting media using Adobe Media Encoder CS5, CS5.5 and CS6, as did Todd Kopriva in Adobe Media Encoder CS5.5: What’s new and changed and (for CS6) Which version of my composition or sequence is used for export using Adobe Media Encoder?.
See also Tutorial: Adobe Media Encoder CS6--UPDATED! by
Jan Ozer at Streaming Media, who doesn't even plug his course at Video2 brain, Producing Great Video with the Adobe Media Encoder. Here's a sample: